fxm3_6 dataset
- graph size: 5026 vertex, 44500 edges
- dataset: square matrix of shortest-path-distances of size 5026 * 5026

Environment
library(bigMap)
# source m.list and graph utilities
source('~/bigMap/bdm_xtrs.R')
# range of perplexities given as a fraction of the number of data rows
ppx.list <- c(.01, .05, .10, .20, .30, .40, .50, .60, .70, .80, .90, .95, .99)
Load Data
load('g.RData')
str(g)
## List of 4
## $ dSet : chr "fxm3_6"
## $ data : int [1:5026, 1:5026] 0 1 1 1 1 1 1 1 1 1 ...
## ..- attr(*, "dimnames")=List of 2
## .. ..$ : NULL
## .. ..$ : chr [1:5026] "V1" "V2" "V3" "V4" ...
## $ edges :'data.frame': 44500 obs. of 2 variables:
## ..$ V1: int [1:44500] 2 3 4 5 6 7 8 9 10 11 ...
## ..$ V2: int [1:44500] 1 1 1 1 1 1 1 1 1 1 ...
## $ is.distance: logi TRUE
Load ptSNE and UMAP results
load('ptSNE_C/glist_C.RData')
g.list <- g.list_C
ptSNE parametric setup
str(g.list[[1]]$ptsne[1:6])
## List of 6
## $ threads: num 6
## $ layers : num 3
## $ rounds : int 4
## $ boost : num 1
## $ theta : num 0
## $ alpha : num 0.5
ptSNE Output
# plot ppx. .01, .05, .10, .20, .30, .50, .50, .70, .90, .95, .99
glist.dev(g.list, method = 'ptsne', path = 'ptSNE_C/', verbose = F)


